Naval Air Facility Atsugi declared all-clear before 2 p.m., and Yokota Air Base, Camp Zama and Yokosuka Naval Base followed suit by late afternoon. Normal operations will resume at the bases on Tuesday.

The storm was moving north toward Miyagi and Fukushima prefectures, the latter of which is the site of the nuclear power plant damaged by the 2011 earthquake and tsunami.

Heavy rain caused massive flooding to the south of Tokyo, with tens of thousands of residents near Kyoto forced to move to higher ground.

On the Kanto Plain, the storm brought winds of up to 50 mph. Sheets of rain, mixed with leaves and small branches, pelted the area from dawn until about noon. By early Monday afternoon, the wind and rain had died out.

Schools were closed at the area bases, and only mission-essential personnel had permission to be outdoors.

Non-essential gates at some bases were closed until the all-clear was declared.

All medical and dental appointments at Yokosuka needed be rescheduled, according to the base’s Facebook site, but its emergency room was open. The base asked all women who are 37 weeks pregnant or more, along with their families, to remain at the hospital while the storm was raging.

The USS Curtis Wilbur and USS Mustin each departed Yokosuka on Saturday in advance of the storm, Task Force 70 spokesman Lt. Cmdr. Paul Macapagal said Monday. Both ships had planned to leave at a later date as part of the aircraft carrier USS George Washington Strike Group. The George Washington departed Friday.

The USS Blue Ridge, which is in port for maintenance, was secured at its pier prior to the storm’s arrival, 7th Fleet officials added.

Japan Rail reported delays on almost all lines running in the Kanto Plain. Service was suspended on all or portions of more than a dozen lines, including the Narita, Ome and Chuo. The closures were for fallen cables and trees, electrical outages and strong winds.

The storm earlier drenched the Kanto Plain all day Sunday with on-and-off downpours.